Workflow

Click the nodes to obtain details about each step.

01 cell ranger

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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sample:
    # Sample name
    sname: "Mix_MM_lines"

# Genome and gff link to create the pre-built Cell Ranger reference
reference:
    link_ref_fasta: "ftp://ftp.ensembl.org/pub/grch37/release-87/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz"
    link_ref_gff: "ftp://ftp.ensembl.org/pub/grch37/release-87/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz"
    # Name for the file of the cellranger reference
    ref_cellranger: "refdata-cellranger-hg19-3.0.0"
    ref_version: "3.0.0"
# parameter for cellranger count
cellranger:
    cells: 5000
    # Restricts cellranger to use specified number of cores to execute pipeline stages
    localcores: 6
    # Restricts cellranger to use specified amount of memory (in GB) to execute pipeline stages.
    localmem: 50

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